morphology_workflows.annotation

Annotation functions.

Module Contents

Functions

assign_mtypes(row, data_dir, mtype_regex=None)	Assign mtype to morphologies.
calculate_y_extent(morph, neurite_type)	Find min/max y value of morphology based on neurite_type.
compute_hard_limits(row, data_dir, skip_axon=False, dendrite_hard_limit='L1_hard_limit', axon_hard_limit='L1_axon_hard_limit')	Compute hard limits.
plot_hard_limits(row, data_dir, with_plotly=True)	Plotting placement annotations on morphologies.
find_apical_point(row, data_dir, tuft_percent=20)	Find apical point.
plot_apical_point(row, data_dir, with_plotly=True)	Plotting apical points on morphologies.
detect_cut_leaves(row, data_dir, bin_width=15, percentile_threshold=75)	Detect cut leaves and save status in df.
plot_cut_leaves(row, data_dir, with_plotly=True)	Plotting cut leaves on morphologies.

morphology_workflows.annotation.logger

morphology_workflows.annotation.assign_mtypes(row, data_dir, mtype_regex=None)

Assign mtype to morphologies.

morphology_workflows.annotation.calculate_y_extent(morph, neurite_type)

Find min/max y value of morphology based on neurite_type.

Taken from morphology_repair_workflow.placement_annotations.py

morphology_workflows.annotation.SEGMENT_TO_NEURITE

morphology_workflows.annotation.compute_hard_limits(row, data_dir, skip_axon=False, dendrite_hard_limit='L1_hard_limit', axon_hard_limit='L1_axon_hard_limit')

Compute hard limits.

morphology_workflows.annotation.plot_hard_limits(row, data_dir, with_plotly=True)

Plotting placement annotations on morphologies.

TODO: update the ploting without plotly.

morphology_workflows.annotation.find_apical_point(row, data_dir, tuft_percent=20)

Find apical point.

morphology_workflows.annotation.plot_apical_point(row, data_dir, with_plotly=True)

Plotting apical points on morphologies.

morphology_workflows.annotation.detect_cut_leaves(row, data_dir, bin_width=15, percentile_threshold=75)

Detect cut leaves and save status in df.

morphology_workflows.annotation.plot_cut_leaves(row, data_dir, with_plotly=True)

Plotting cut leaves on morphologies.